Is it happening on all subjects or just some of them?

On 01/11/2017 03:45 PM, Jamie Hanson wrote:

Apologies my email must have clipped it out.
I pasted it below.



=======

Hello Freesurfer List,

I was running into issues processing subjects, with errors just getting through the autorecon1 step of the pipeline. My terminal outputs the following:

====

/home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/mri
/usr/local/pkg/freesurfer-dev//bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Tue Jan 10 12:53:44 EST 2017
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.129237
/home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.129237/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.129237/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.32349e-23, -1.32349e-23)
j_ras = (0, 1.49012e-08, -1)
k_ras = (0, 1, 1.49012e-08)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.129237/nu0.mnc...

--------------------------------------------------------
Iteration 1 Tue Jan 10 12:53:47 EST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.129237/nu0.mnc ./tmp.mri_nu_correct.mni.129237/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.129237/0/ -iterations 1000 -distance 50
Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/pkg/freesurfer//mni/bin/nu_estimate_np_and_em line 165.
nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280)
ERROR: nu_correct
Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 10007 exited with ERRORS at Tue Jan 10 12:53:47 EST 2017

For more details, see the log file /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/scripts/recon-all.log

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>

====

Searching the FS list, I saw that I originally thought this was an incompatibility with the current stable Freesurfer version and the most recent MNI tools. To troubleshoot that issue, I installed the dev version of Freesurfer (as noted by this thread: https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2016-September/047734.html <https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2016-September/047734.html>). The error however still persists (even using the dev version). Anyone else run into this issue or have thoughts about troubleshooting it? Thanks much!

Best,
Jamie.

--
Jamie Hanson
Assistant Professor, Psychology
Research Scientist, Learning Research and Development Center
University of Pittsburgh
Personal website: jamiehanson.org <http://jamiehanson.org/>


On Wed, Jan 11, 2017 at 3:42 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    please include previous correspondence. we get a lot of emails
    here and can't remember the context of each one.

    thanks


    On 01/11/2017 03:17 PM, Jamie Hanson wrote:


        I'm seeing it for multiple subjects, same issue. I can't get
        passed the autorecon1 steps. Any thoughts?


    --     Douglas N. Greve, Ph.D.
    MGH-NMR Center
    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    Phone Number: 617-724-2358 <tel:617-724-2358>
    Fax: 617-726-7422 <tel:617-726-7422>

    Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
    FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
    <https://gate.nmr.mgh.harvard.edu/filedrop2>
    www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
    Outgoing:
    ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
    <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>



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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/